/// <summary>
/// calculates the cDNA coordinates given the specified genomic coordinates [Transcript.pm:927 cdna_coding_start]
/// genomic2pep [TransciptMapper:482]
/// </summary>
public static void GetCodingDnaEndpoints(CdnaCoordinateMap[] cdnaMaps, int genomicBegin, int genomicEnd, out int cdnaBegin, out int cdnaEnd)
{
// find an overlapping mapper pair
var coordinateMap = CdnaCoordinateMap.Null();
bool foundOverlap = false;
for (int i = 0; i < cdnaMaps.Length; i++)
{
coordinateMap = cdnaMaps[i];
if (genomicEnd >= coordinateMap.GenomicStart &&
genomicBegin <= coordinateMap.GenomicEnd)
{
foundOverlap = true;
break;
}
}
if (!foundOverlap)
{
throw new GeneralException($"Unable to find an overlapping mapping pair for these genomic coordinates: ({genomicBegin}, {genomicEnd})");
}
// calculate the cDNA position
cdnaBegin = coordinateMap.CdnaEnd - (genomicEnd - coordinateMap.GenomicStart);
cdnaEnd = coordinateMap.CdnaEnd - (genomicBegin - coordinateMap.GenomicStart);
}
/// <summary>
/// sets both the exon and intron number strings according to which were affected by the variant [BaseTranscriptVariation.pm:474 _exon_intron_number]
/// </summary>
public static void ExonIntronNumber(CdnaCoordinateMap[] cdnaMaps, SimpleInterval[] introns, bool onReverseStrand,
TranscriptAnnotation ta, out string exonNumber, out string intronNumber)
{
int exonCount = 0;
var altAllele = ta.AlternateAllele;
var variantInterval = new AnnotationInterval(altAllele.Start, altAllele.End);
var overlappedExons = new List <int>();
var overlappedIntrons = new List <int>();
var prevExon = CdnaCoordinateMap.Null();
foreach (var exon in cdnaMaps)
{
exonCount++;
if (variantInterval.Overlaps(exon.GenomicStart, exon.GenomicEnd))
{
overlappedExons.Add(exonCount);
}
if (!prevExon.IsNull)
{
int intronStart = prevExon.GenomicEnd + 1;
int intronEnd = exon.GenomicStart - 1;
if (variantInterval.Overlaps(intronStart, intronEnd))
{
overlappedIntrons.Add(exonCount - 1);
}
}
prevExon = exon;
}
exonNumber = GetExonIntronNumber(overlappedExons, cdnaMaps.Length, onReverseStrand);
intronNumber = introns != null?GetExonIntronNumber(overlappedIntrons, introns.Length, onReverseStrand) : null;
if (overlappedExons.Count > 0)
{
ta.HasExonOverlap = true;
}
}